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Kong D, Xu L, Dai M, Ye Z, Ma B, Tan X. Deciphering the functional assembly of microbial communities driven by heavy metals in the tidal soils of Hangzhou Bay. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124671. [PMID: 39116926 DOI: 10.1016/j.envpol.2024.124671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Understanding the interaction between heavy metals and soil microbiomes is essential for maintaining ecosystem health and functionality in the face of persistent human-induced challenges. This study investigated the complex relationships between heavy metal contamination and the functional characteristics of soil microbial communities in the tidal soils of Hangzhou Bay, a region experiencing substantial environmental pressure due to its proximity to densely populated and industrialized regions. The north-shore sampling site showed moderate contaminations (mg/kg) of total arsenic (16.61 ± 1.13), cadmium (0.3 ± 0.05), copper (31.28 ± 1.23), nickel (37.44 ± 2.74), lead (34.29 ± 5.99), and zinc (120.8 ± 5.96), which are 1.29-2.94 times higher than the geochemical background values in Hangzhou Bay and adjacent areas. In contrast, the south-shore sampling site showed slightly higher levels of total arsenic (13.76 ± 1.35) and cadmium (0.13 ± 0.02) than the background values. Utilizing metagenomic sequencing, we decoded microbial functional genes essential for nitrogen, phosphorus, sulfur, and methane biogeochemical cycles. Although soil available nickel content was relatively low at 1 mg/kg, it exhibited strong associations with diverse microbial genes and biogeochemical pathways. Four key genes-hxlB, glpX, opd, and phny-emerged as pivotal players in the interactions with available nickel, suggesting the adaptability of microbial metabolic responses to heavy metal. Additionally, microbial genera such as Gemmatimonas and Ilumatobacter, which harbored diverse functional genes, demonstrated potential interactions with soil nickel. These findings highlight the importance of understanding heavy metal-soil microbiome dynamics for effective environmental management strategies in the tidal soils of Hangzhou Bay, with the goal of preserving ecosystem health and functionality amidst ongoing anthropogenic challenges.
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Affiliation(s)
- Dedong Kong
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Linya Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Nantong Cultivated Land Quality Protection Station, Nantong, Jiangsu, 226001, China
| | - Mengdi Dai
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ziran Ye
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Guan X, Jia D, Liu X, Ding C, Guo J, Yao M, Zhang Z, Zhou M, Sun J. Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173772. [PMID: 38871313 DOI: 10.1016/j.scitotenv.2024.173772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.
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Affiliation(s)
- Xin Guan
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Dai Jia
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China.
| | - Xinyu Liu
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Changling Ding
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China; Institute for Advanced Marine Research, China University of Geosciences (Wuhan), Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
| | - Jinfei Guo
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Min Yao
- Jiangsu Hydrology and Water Resources Survey Bureau, Nanjing, China
| | - Zhan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Mengxi Zhou
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China; Institute for Advanced Marine Research, China University of Geosciences (Wuhan), Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China.
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Rekadwad BN, Shouche YS, Jangid K. A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea. BMC Microbiol 2024; 24:162. [PMID: 38730339 PMCID: PMC11084130 DOI: 10.1186/s12866-024-03295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris. RESULTS The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study. CONCLUSION Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- National Centre for Microbial Resource, DBT - National Centre for Cell Science (DBT-NCCS), NCCS-Complex, Savitribai Phule Pune University (SPPU) Campus, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India.
| | - Yogesh Shreepad Shouche
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India
- Gut Microbiology Research Division, SKAN Research Trust, Bangalore, Karnataka, 560034, India
| | - Kamlesh Jangid
- Bioenergy Group, DST-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, Maharashtra, 411 004, India
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McGrath AH, Lema K, Egan S, Wood G, Gonzalez SV, Kjelleberg S, Steinberg PD, Marzinelli EM. Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont. NPJ Biofilms Microbiomes 2024; 10:33. [PMID: 38553475 PMCID: PMC10980776 DOI: 10.1038/s41522-024-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.
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Affiliation(s)
- Alexander Harry McGrath
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia.
- Sydney Institute of Marine Science, Mosman, NSW, Australia.
| | - Kimberley Lema
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Georgina Wood
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- UWA Oceans Institute & School of Biological Sciences, Indian Ocean Marine Research Centre, The University of Western Australia, Sydney, Australia
| | - Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
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Orel N, Fadeev E, Herndl GJ, Turk V, Tinta T. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics 2024; 25:146. [PMID: 38321410 PMCID: PMC10845552 DOI: 10.1186/s12864-024-10062-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. RESULTS We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. CONCLUSIONS Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
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6
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Prasoodanan P K V, Kumar S, Dhakan DB, Waiker P, Saxena R, Sharma VK. Metagenomic exploration of Andaman region of the Indian Ocean. Sci Rep 2024; 14:2717. [PMID: 38302544 PMCID: PMC10834444 DOI: 10.1038/s41598-024-53190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/28/2024] [Indexed: 02/03/2024] Open
Abstract
Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.
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Affiliation(s)
- Vishnu Prasoodanan P K
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sudhir Kumar
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Darshan B Dhakan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Prashant Waiker
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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Graham OJ, Adamczyk EM, Schenk S, Dawkins P, Burke S, Chei E, Cisz K, Dayal S, Elstner J, Hausner ALP, Hughes T, Manglani O, McDonald M, Mikles C, Poslednik A, Vinton A, Wegener Parfrey L, Harvell CD. Manipulation of the seagrass-associated microbiome reduces disease severity. Environ Microbiol 2024; 26:e16582. [PMID: 38195072 DOI: 10.1111/1462-2920.16582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.
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Affiliation(s)
- Olivia J Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily M Adamczyk
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siobhan Schenk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phoebe Dawkins
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Samantha Burke
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily Chei
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kaitlyn Cisz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Sukanya Dayal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jack Elstner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Taylor Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Omisha Manglani
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Miles McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Chloe Mikles
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Anna Poslednik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Audrey Vinton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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Tasdemir D, Scarpato S, Utermann-Thüsing C, Jensen T, Blümel M, Wenzel-Storjohann A, Welsch C, Echelmeyer VA. Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168422. [PMID: 37956849 DOI: 10.1016/j.scitotenv.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.
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Affiliation(s)
- Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany; Faculty of Mathematics and Natural Sciences, Kiel University, Kiel 24118, Germany.
| | - Silvia Scarpato
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Caroline Utermann-Thüsing
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Timo Jensen
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Arlette Wenzel-Storjohann
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Claudia Welsch
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Vivien Anne Echelmeyer
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
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9
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Jin J, Yamamoto R, Shiroguchi K. High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ. Nat Protoc 2024; 19:207-239. [PMID: 38012397 DOI: 10.1038/s41596-023-00906-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/24/2023] [Indexed: 11/29/2023]
Abstract
Bacteria often function as a community, called the microbiota, consisting of many different bacterial species. The accurate identification of bacterial types and the simultaneous quantification of the cells of each bacterial type will advance our understanding of microbiota; however, this cannot be performed by conventional 16S rRNA sequencing methods as they only identify and quantify genes, which do not always represent cells. Here, we present a protocol for our developed method, barcoding bacteria for identification and quantification (BarBIQ). In BarBIQ, the 16S rRNA genes of single bacterial cells are amplified and attached to a unique cellular barcode in a droplet. Sequencing the tandemly linked cellular barcodes and 16S rRNA genes from many droplets (representing many cells with unique cellular barcodes) and clustering the sequences using the barcodes determines both the bacterial type for each cell based on 16S rRNA gene and the number of cells for each bacterial type based on the quantity of barcode types sequenced. Single-base accuracy for 16S rRNA sequencing is achieved via the barcodes and by avoiding chimera formation from 16S rRNA genes of different bacteria using droplets. For data processing, an easy-to-use bioinformatic pipeline is available ( https://github.com/Shiroguchi-Lab/BarBIQ_Pipeline_V1_2_0 ). This protocol allows researchers with experience in molecular biology but without bioinformatics experience to perform the process in ~2 weeks. We show the application of BarBIQ in mouse gut microbiota analysis as an example; however, this method is also applicable to other microbiota samples, including those from the mouth and skin, marine environments, soil and plants, as well as those from other terrestrial environments.
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Affiliation(s)
- Jianshi Jin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China.
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan.
| | - Reiko Yamamoto
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
| | - Katsuyuki Shiroguchi
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan.
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10
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Elsherbini J, Corzett C, Ravaglioli C, Tamburello L, Polz M, Bulleri F. Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels. MICROBIAL ECOLOGY 2023; 86:1552-1564. [PMID: 36790500 PMCID: PMC10497455 DOI: 10.1007/s00248-023-02174-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.
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Affiliation(s)
- Joseph Elsherbini
- MIT Microbiology Graduate Program, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02138, USA
| | - Christopher Corzett
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chiara Ravaglioli
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy
| | - Laura Tamburello
- Department of Integrative Marine Ecology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, 80077, Punta San Pietro, Ischia, (Naples), Italy
| | - Martin Polz
- MIT Microbiology Graduate Program, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02138, USA
- Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1130, Vienna, Austria
| | - Fabio Bulleri
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy.
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11
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Desdouits M, Reynaud Y, Philippe C, Guyader FSL. A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish. Microorganisms 2023; 11:2218. [PMID: 37764063 PMCID: PMC10537662 DOI: 10.3390/microorganisms11092218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Unité Microbiologie Aliment Santé et Environnement, RBE/LSEM, 44311 Nantes, France; (M.D.); (Y.R.); (C.P.)
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12
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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13
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Liang H, Wang L, Wang S, Sun D, Li J, Xu Y, Zhang H. Remote sensing detection of seagrass distribution in a marine lagoon (Swan Lake), China. OPTICS EXPRESS 2023; 31:27677-27695. [PMID: 37710838 DOI: 10.1364/oe.498901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/24/2023] [Indexed: 09/16/2023]
Abstract
Seagrass, a submerged flowering plant, is widely distributed in coastal shallow waters and plays a significant role in maintaining marine biodiversity and carbon cycles. However, the seagrass ecosystem is currently facing degradation, necessitating effective monitoring. Satellite remote sensing observations offer distinct advantages in spatial coverage and temporal frequency. In this study, we focused on a marine lagoon (Swan Lake), located in the Shandong Peninsula of China which is characterized by a large and typical seagrass population. We conducted an analysis of remote sensing reflectance of seagrass and other objectives using a comprehensive Landsat satellite dataset spanning from 2002 to 2022. Subsequently, we constructed Seagrass Index I (SSI-I) and Seagrass Index II (SSI-II), and used them to develop a stepwise model for seagrass detection from Landsat images. Validation was performed using in situ acoustic survey data and visual interpretation, revealing the good performance of our model with an overall accuracy exceeding 0.90 and a kappa coefficient around 0.80. The long-term analysis (2002-2022) of the seagrass distribution area in Swan Lake, generated from Landsat data using our model, indicated that the central area of Swan Lake sustains seagrass for the longest duration. Seagrass in Swan Lake exhibits a regular seasonal variation, including seeding in early spring, growth in spring-summer, maturation in the middle of summer, and shrinkage in autumn. Furthermore, we observed an overall decreasing trend in the seagrass area over the past 20 years, while occasional periods of seagrass restoration were also observed. These findings provide crucial information for seagrass protection, marine blue carbon studies, and related endeavors in Swan Lake. Moreover, our study offers a valuable alternative approach that can be implemented for seagrass monitoring using satellite observations in other coastal regions.
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14
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Watson SM, McLean DL, Balcom BJ, Birchenough SNR, Brand AM, Camprasse ECM, Claisse JT, Coolen JWP, Cresswell T, Fokkema B, Gourvenec S, Henry LA, Hewitt CL, Love MS, MacIntosh AE, Marnane M, McKinley E, Micallef S, Morgan D, Nicolette J, Ounanian K, Patterson J, Seath K, Selman AGL, Suthers IM, Todd VLG, Tung A, Macreadie PI. Offshore decommissioning horizon scan: Research priorities to support decision-making activities for oil and gas infrastructure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163015. [PMID: 36965737 DOI: 10.1016/j.scitotenv.2023.163015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 05/13/2023]
Abstract
Thousands of oil and gas structures have been installed in the world's oceans over the past 70 years to meet the population's reliance on hydrocarbons. Over the last decade, there has been increased concern over how to handle decommissioning of this infrastructure when it reaches the end of its operational life. Complete or partial removal may or may not present the best option when considering potential impacts on the environment, society, technical feasibility, economy, and future asset liability. Re-purposing of offshore structures may also be a valid legal option under international maritime law where robust evidence exists to support this option. Given the complex nature of decommissioning offshore infrastructure, a global horizon scan was undertaken, eliciting input from an interdisciplinary cohort of 35 global experts to develop the top ten priority research needs to further inform decommissioning decisions and advance our understanding of their potential impacts. The highest research priorities included: (1) an assessment of impacts of contaminants and their acceptable environmental limits to reduce potential for ecological harm; (2) defining risk and acceptability thresholds in policy/governance; (3) characterising liability issues of ongoing costs and responsibility; and (4) quantification of impacts to ecosystem services. The remaining top ten priorities included: (5) quantifying ecological connectivity; (6) assessing marine life productivity; (7) determining feasibility of infrastructure re-use; (8) identification of stakeholder views and values; (9) quantification of greenhouse gas emissions; and (10) developing a transdisciplinary decommissioning decision-making process. Addressing these priorities will help inform policy development and governance frameworks to provide industry and stakeholders with a clearer path forward for offshore decommissioning. The principles and framework developed in this paper are equally applicable for informing responsible decommissioning of offshore renewable energy infrastructure, in particular wind turbines, a field that is accelerating rapidly.
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Affiliation(s)
- Sarah M Watson
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - Dianne L McLean
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Perth, Western Australia 6009, Australia; Oceans Institute, The University of Western Australia, Perth, Western Australia 6009, Australia.
| | | | - Silvana N R Birchenough
- The Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft NR33 0HT, United Kingdom
| | - Alison M Brand
- Manta Environmental Limited, Aberdeen, Scotland, United Kingdom
| | - Elodie C M Camprasse
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - Jeremy T Claisse
- California State Polytechnic University, Pomona, CA 91786, USA; Vantuna Research Group, Occidental College, Los Angeles, CA 90041, USA
| | | | - Tom Cresswell
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, New South Wales 2234, Australia
| | - Bert Fokkema
- Shell Global Solutions International B.V., 2596HR The Hague, the Netherlands
| | - Susan Gourvenec
- Centre of Excellence for Intelligent & Resilient Ocean Engineering, University of Southampton, Southampton SO16 7QF, UK
| | - Lea-Anne Henry
- School of GeoSciences, University of Edinburgh, King's Buildings Campus, James Hutton Road, EH9 3FE Edinburgh, United Kingdom
| | - Chad L Hewitt
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia; Lincoln University, Lincoln, New Zealand
| | - Milton S Love
- Marine Science Institute, University of California, Santa Barbara, CA 93016, USA
| | - Amy E MacIntosh
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, New South Wales 2234, Australia; School of Natural Sciences, Macquarie University, Macquarie Park, Sydney, New South Wales 2109, Australia
| | - Michael Marnane
- Chevron Energy Technology Pty Ltd, 250 St Georges Terrace, Perth, Western Australia 6000, Australia
| | - Emma McKinley
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Shannon Micallef
- Department of Climate Change, Energy, the Environment and Water, Australia
| | - Deborah Morgan
- Xodus Group, Xodus House, Huntly Street, Aberdeen AB10 1RS, Scotland, United Kingdom
| | - Joseph Nicolette
- Montrose Environmental Solutions Inc., Northridge Road, Sandy Springs, GA 30350, USA
| | - Kristen Ounanian
- Centre for Blue Governance, Aalborg University, Aalborg, Denmark
| | | | - Karen Seath
- Society for Underwater Technology, International Salvage & Decommissioning Committee, UK; Karen Seath Solutions, Anstruther, Scotland, UK
| | - Allison G L Selman
- Asset Lifecycle Manager, Atteris Pty Ltd, Perth, Western Australia 6000, Australia
| | - Iain M Suthers
- School of Biological, Earth & Environmental Science, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Victoria L G Todd
- Ocean Science Consulting Ltd., Spott Road, Dunbar, East Lothian EH42 1RR, Scotland, United Kingdom
| | - Aaron Tung
- University of Aberdeen, School of Law, Aberdeen, UK; Curtin Institute for Energy Transition, Technology Park, Bentley, Western Australia 6102, Australia; Woodside Energy, Mia Yellagonga, 11 Mount Street, Perth, Western Australia 6000, Australia
| | - Peter I Macreadie
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC 3125, Australia
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15
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Chen B, Zhang Z, Wang T, Hu H, Qin G, Lu T, Hong W, Hu J, Penuelas J, Qian H. Global distribution of marine microplastics and potential for biodegradation. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131198. [PMID: 36921415 DOI: 10.1016/j.jhazmat.2023.131198] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.
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Affiliation(s)
- Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Hang Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Jun Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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16
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Deb M, Redkar N, Manohar CS, Jagtap AS, Saxena S, Shukla S. Bacillussp. based nano-bio hybrids for efficient water remediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121490. [PMID: 36965681 DOI: 10.1016/j.envpol.2023.121490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Macroalgae are a diverse group of primary producers that offer indispensable ecosystem services towards bacterial colonization and proliferation in aquatic biomes. Macroalgae/bacteria interactions are complex in natural biomes and contribute mutually to their growth and biotechnological outcomes. Most findings on macroalgae-associated bacteria and their secreted enzymes have largely been limited to nutraceutical applications. Here, in this study, we demonstrate and investigate the growth of Bacillus sp. (macroalgae-associated bacteria) with the substitution of its associated macroalgae (Gracilaria corticata) on graphene oxide (GO). The findings indicated that the presence of wrinkles of GO nanosheets resulted in cell proliferation and adherence without causing mechanical damage to the cell membrane. Furthermore, the assembly of GO-marine bacteria was explored for organic pollutant treatment using methylene blue (MB) as a model dye. The degradation results suggest the breakdown of MB into non-toxic byproducts as suggested by the phytotoxicity assay.
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Affiliation(s)
- Madhurima Deb
- Nanostructures Engineering and Modeling Laboratory, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai, 400076, India; Centre for Research in Nano Technology and Science, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Neha Redkar
- Nanostructures Engineering and Modeling Laboratory, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Cathrine Sumathi Manohar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Ashok Shivaji Jagtap
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Sumit Saxena
- Nanostructures Engineering and Modeling Laboratory, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai, 400076, India; Water Innovation Centre: Technology, Research & Education (WICTRE), Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shobha Shukla
- Nanostructures Engineering and Modeling Laboratory, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai, 400076, India; Water Innovation Centre: Technology, Research & Education (WICTRE), Indian Institute of Technology Bombay, Mumbai, 400076, India.
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17
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Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE, Lee JN, Yeo ZY, Zahn G. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival. ENVIRONMENTAL MICROBIOME 2023; 18:47. [PMID: 37264467 DOI: 10.1186/s40793-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/01/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival. CONCLUSION The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.
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Affiliation(s)
- Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Trevor Millar
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lacee Bowen
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lauren Semon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Zhi Yi Yeo
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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18
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Guajardo-Leiva S, Mendez KN, Meneses C, Díez B, Castro-Nallar E. A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S). Microorganisms 2023; 11:microorganisms11040904. [PMID: 37110327 PMCID: PMC10143455 DOI: 10.3390/microorganisms11040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Claudio Meneses
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 7800003, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
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Habibi N, Uddin S, Al-Sarawi H, Aldhameer A, Shajan A, Zakir F, Abdul Razzack N, Alam F. Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome. Microorganisms 2023; 11:microorganisms11020531. [PMID: 36838497 PMCID: PMC9960530 DOI: 10.3390/microorganisms11020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
- Correspondence:
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Hanan Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Ahmed Aldhameer
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Faiz Alam
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
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20
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Rowland JA, Walsh JC, Beitzel M, Brawata R, Brown D, Chalmers L, Evans L, Eyles K, Gibbs R, Grover S, Grundy S, Harris RMB, Haywood S, Hilton M, Hope G, Keaney B, Keatley M, Keith DA, Lawrence R, Lutz ML, MacDonald T, MacPhee E, McLean N, Powell S, Robledo‐Ruiz DA, Sato CF, Schroder M, Silvester E, Tolsma A, Western AW, Whinam J, White M, Wild A, Williams RJ, Wright G, Young W, Moore JL. Setting research priorities for effective management of a threatened ecosystem: Australian alpine and subalpine peatland. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Jessica A. Rowland
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Jessica C. Walsh
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Matthew Beitzel
- Conservation Research, Environment, Planning and Sustainable Development Directorate Canberra Australia
| | - Renee Brawata
- Conservation Research, Environment, Planning and Sustainable Development Directorate Canberra Australia
| | - Daniel Brown
- Eastern Victoria Office Bright Victoria Australia
| | - Linden Chalmers
- Biodiversity Planning and Policy, ACT Government Dickson Australia
| | - Lisa Evans
- Conservation Research, Environment, Planning and Sustainable Development Directorate Canberra Australia
| | - Kathryn Eyles
- Department of Climate Change, Energy, and the Environment Canberra Australia
| | - Rob Gibbs
- Australian Alps National Parks Co‐operative Management Program, NSW National Parks and Wildlife Service, Department of Planning, Industry and Environment Parramatta New South Wales Australia
| | - Samantha Grover
- Applied Chemistry and Environmental Science RMIT University Melbourne Victoria Australia
| | - Shane Grundy
- International Mire Conservation Group (IMCG) Greifswald Germany
| | - Rebecca M. B. Harris
- School of Geography, Planning, and Spatial Sciences University of Tasmania Hobart Tasmania Australia
| | - Shayne Haywood
- West Gippsland Catchment Management Authority Traralgon Victoria Australia
| | - Mairi Hilton
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Geoffrey Hope
- College of Asia and the Pacific, Australian National University Canberra Australia
| | - Ben Keaney
- College of Asia and the Pacific, Australian National University Canberra Australia
| | | | - David A. Keith
- Centre for Ecosystem Science, University of New South Wales Sydney New South Wales Australia
- NSW Department of Planning, Industry and Environment Hurstville New South Wales Australia
| | - Ruth Lawrence
- Department of Geography The University of Melbourne Carlton Victoria Australia
| | - Maiko L. Lutz
- School of Biological Sciences Monash University Clayton Victoria Australia
| | | | - Elizabeth MacPhee
- Alpine Flora ‐ High Altitude Rehabilitation Consultant Tumut New South Wales Australia
| | - Nina McLean
- Conservation Research, Environment, Planning and Sustainable Development Directorate Canberra Australia
| | - Susan Powell
- Department of Climate Change, Energy, and the Environment Canberra Australia
| | | | - Chloe F. Sato
- ACT Government Canberra Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University Burwood Victoria Australia
| | - Mel Schroder
- Southern Ranges Branch, NSW National Parks and Wildlife Service, Department of Planning, Industry and Environment Jindabyne New South Wales Australia
| | - Ewen Silvester
- Research Centre for Applied Alpine Ecology (RCAAE), Department of Ecology, Environment and Evolution (DEEE) La Trobe University Wodonga Australia
| | - Arn Tolsma
- Arthur Rylah Institute, Biodiversity Division, Environment and Climate Change, Department of Environment, Land, Water and Planning Heidelberg Victoria Australia
| | - Andrew W. Western
- Department of Infrastructure Engineering The University of Melbourne Parkville Australia
| | - Jennie Whinam
- School of Geography, Planning & Spatial Sciences University of Tasmania Sandy Bay Tasmania Australia
| | - Matthew White
- Biodiversity Conservation Division, Department of Agriculture, Water and the Environment Canberra Australia
| | - Anita Wild
- Wild Ecology Pty Ltd. Mount Nelson Tasmania Australia
| | - Richard J. Williams
- Charles Darwin University Faculty of Engineering Health Science and the Environment, Institute for the Environment and Livelihoods Darwin Northwest Territories Australia
| | - Genevieve Wright
- NSW Department of Planning, Industry and Environment Hurstville New South Wales Australia
| | - Wade Young
- Parks and Conservation Service, Environment and Planning Directorate Canberra Australia
| | - Joslin L. Moore
- School of Biological Sciences Monash University Clayton Victoria Australia
- Arthur Rylah Institute, Biodiversity Division, Environment and Climate Change, Department of Environment, Land, Water and Planning Heidelberg Victoria Australia
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21
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Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies. Biotechniques 2022; 73:183-191. [PMID: 36189957 PMCID: PMC9623733 DOI: 10.2144/btn-2022-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.
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22
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Beatty DS, Aoki LR, Rappazzo B, Bergman C, Domke LK, Duffy JE, Dubois K, Eckert GL, Gomes C, Graham OJ, Harper L, Harvell CD, Hawthorne TL, Hessing-Lewis M, Hovel K, Monteith ZL, Mueller RS, Olson AM, Prentice C, Tomas F, Yang B, Stachowicz JJ. Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific. mSystems 2022; 7:e0022422. [PMID: 35856664 PMCID: PMC9426469 DOI: 10.1128/msystems.00224-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Predicting outcomes of marine disease outbreaks presents a challenge in the face of both global and local stressors. Host-associated microbiomes may play important roles in disease dynamics but remain understudied in marine ecosystems. Host-pathogen-microbiome interactions can vary across host ranges, gradients of disease, and temperature; studying these relationships may aid our ability to forecast disease dynamics. Eelgrass, Zostera marina, is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae. We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We detected effects of geography (11%) and smaller, but distinct, effects of temperature (30-day max sea surface temperature, 4%) and disease (lesion prevalence, 3%) on microbiome composition. Declines in alpha diversity on asymptomatic tissue occurred with rising wasting disease prevalence within meadows. However, no change in microbiome variability (dispersion) was detected between asymptomatic and symptomatic tissues. Further, we identified members of Cellvibrionaceae, Colwelliaceae, and Granulosicoccaceae on asymptomatic tissue that are predictive of wasting disease prevalence across the geographic range (3,100 kilometers). Functional roles of Colwelliaceae and Granulosicoccaceae are not known. Cellvibrionaceae, degraders of plant cellulose, were also enriched in lesions and adjacent green tissue relative to nonlesioned leaves. Cellvibrionaceae may play important roles in disease progression by degrading host tissues or overwhelming plant immune responses. Thus, inclusion of microbiomes in wasting disease studies may improve our ability to understand variable rates of infection, disease progression, and plant survival. IMPORTANCE The roles of marine microbiomes in disease remain poorly understood due, in part, to the challenging nature of sampling at appropriate spatiotemporal scales and across natural gradients of disease throughout host ranges. This is especially true for marine vascular plants like eelgrass (Zostera marina) that are vital for ecosystem function and biodiversity but are susceptible to rapid decline and die-off from pathogens like eukaryotic slime-mold Labyrinthula zosterae (wasting disease). We link bacterial members of phyllosphere tissues to the prevalence of wasting disease across the broadest geographic range to date for a marine plant microbiome-disease study (3,100 km). We identify Cellvibrionaceae, plant cell wall degraders, enriched (up to 61% relative abundance) within lesion tissue, which suggests this group may be playing important roles in disease progression. These findings suggest inclusion of microbiomes in marine disease studies will improve our ability to predict ecological outcomes of infection across variable landscapes spanning thousands of kilometers.
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Affiliation(s)
- Deanna S. Beatty
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Lillian R. Aoki
- Data Science Initiative, University of Oregon, Eugene, Oregon, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Brendan Rappazzo
- Department of Computer Science, Cornell University, Ithaca, New York, USA
| | - Chelsea Bergman
- Department of Biology and Coastal & Marine Institute, San Diego State University, San Diego, California, USA
| | - Lia K. Domke
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - J. Emmett Duffy
- MarineGEO Program and Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Katie Dubois
- Department of Evolution and Ecology, University of California, Davis, California, USA
- Biology Department, Bowdoin College, Brunswick, Maine, USA
| | - Ginny L. Eckert
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Carla Gomes
- Department of Computer Science, Cornell University, Ithaca, New York, USA
| | - Olivia J. Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Leah Harper
- MarineGEO Program and Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - C. Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Timothy L. Hawthorne
- Department of Sociology and College of Sciences GIS Cluster, University of Central Florida, Orlando, Florida, USA
| | - Margot Hessing-Lewis
- Nearshore Marine Ecology, Hakai Institute, Heriot Bay, British Columbia, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Hovel
- Department of Biology and Coastal & Marine Institute, San Diego State University, San Diego, California, USA
| | - Zachary L. Monteith
- Nearshore Marine Ecology, Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Ryan S. Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Angeleen M. Olson
- Nearshore Marine Ecology, Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Carolyn Prentice
- Nearshore Marine Ecology, Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Fiona Tomas
- Instituto Mediterráneo de Estudios Avanzados (UIB-CSIC), Esporles, Spain
| | - Bo Yang
- Department of Sociology and College of Sciences GIS Cluster, University of Central Florida, Orlando, Florida, USA
- Department of Urban and Regional Planning, San Jose State University, San Jose, California, USA
| | - John J. Stachowicz
- Department of Evolution and Ecology, University of California, Davis, California, USA
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23
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Eger AM, Marzinelli EM, Christie H, Fagerli CW, Fujita D, Gonzalez AP, Hong SW, Kim JH, Lee LC, McHugh TA, Nishihara GN, Tatsumi M, Steinberg PD, Vergés A. Global kelp forest restoration: past lessons, present status, and future directions. Biol Rev Camb Philos Soc 2022; 97:1449-1475. [PMID: 35255531 PMCID: PMC9543053 DOI: 10.1111/brv.12850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
Kelp forest ecosystems and their associated ecosystem services are declining around the world. In response, marine managers are working to restore and counteract these declines. Kelp restoration first started in the 1700s in Japan and since then has spread across the globe. Restoration efforts, however, have been largely disconnected, with varying methodologies trialled by different actors in different countries. Moreover, a small subset of these efforts are 'afforestation', which focuses on creating new kelp habitat, as opposed to restoring kelp where it previously existed. To distil lessons learned over the last 300 years of kelp restoration, we review the history of kelp restoration (including afforestation) around the world and synthesise the results of 259 documented restoration attempts spanning from 1957 to 2020, across 16 countries, five languages, and multiple user groups. Our results show that kelp restoration projects have increased in frequency, have employed 10 different methodologies and targeted 17 different kelp genera. Of these projects, the majority have been led by academics (62%), have been conducted at sizes of less than 1 ha (80%) and took place over time spans of less than 2 years. We show that projects are most successful when they are located near existing kelp forests. Further, disturbance events such as sea-urchin grazing are identified as regular causes of project failure. Costs for restoration are historically high, averaging hundreds of thousands of dollars per hectare, therefore we explore avenues to reduce these costs and suggest financial and legal pathways for scaling up future restoration efforts. One key suggestion is the creation of a living database which serves as a platform for recording restoration projects, showcasing and/or re-analysing existing data, and providing updated information. Our work establishes the groundwork to provide adaptive and relevant recommendations on best practices for kelp restoration projects today and into the future.
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Affiliation(s)
- Aaron M. Eger
- Centre for Marine Science and Innovation & Ecology and Evolution Research Centre, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNSW2052
| | - Ezequiel M. Marzinelli
- The University of Sydney, School of Life and Environmental SciencesSydneyNSW2006Australia
- Sydney Institute of Marine Science19 Chowder Bay RdMosmanNSW2088Australia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingapore637551Singapore
| | - Hartvig Christie
- Norwegian Institute for Water ResearchØkernveien 94Oslo0579Norway
| | | | - Daisuke Fujita
- University of Tokyo Marine Science and Technology, School of Marine Bioresources, Applied PhycologyKonan, Minato‐kuTokyo108‐8477Japan
| | - Alejandra P. Gonzalez
- Departamento de Ciencias Ecológicas, Facultad de CienciasUniversidad de ChileLas Palmeras 3425, ÑuñoaSantiagoChile
| | - Seok Woo Hong
- Department of Biological SciencesSungkyunkwan UniversitySuwon2066South Korea
| | - Jeong Ha Kim
- Department of Biological SciencesSungkyunkwan UniversitySuwon2066South Korea
| | - Lynn C. Lee
- Gwaii Haanas National Park Reserve, National Marine Conservation Area Reserve, and Haida Heritage Site60 Second Beach Road, SkidegateHaida GwaiiBCV0T 1S1Canada
- Canada & School of Environmental Sciences, University of Victoria3800 Finnerty RoadVictoriaBCV8P 5C2Canada
| | - Tristin Anoush McHugh
- Reef Check Foundation, Long Marine Laboratory115 McAllister RoadSanta CruzCA95060U.S.A.
- Present address:
The Nature Conservancy830 S StreetSacramentoCA95811U.S.A.
| | - Gregory N. Nishihara
- Organization for Marine Science and TechnologyInstitute for East China Sea Research, Nagasaki University1551‐7 Taira‐machiNagasaki City851‐2213Japan
| | - Masayuki Tatsumi
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTAS7004Australia
| | - Peter D. Steinberg
- Centre for Marine Science and Innovation & Ecology and Evolution Research Centre, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNSW2052
- Sydney Institute of Marine Science19 Chowder Bay RdMosmanNSW2088Australia
| | - Adriana Vergés
- Centre for Marine Science and Innovation & Ecology and Evolution Research Centre, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNSW2052
- Sydney Institute of Marine Science19 Chowder Bay RdMosmanNSW2088Australia
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24
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Abstract
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.
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25
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Changes in Temporal Dynamics and Factors Influencing the Environment of the Bacterial Community in Mangrove Rhizosphere Sediments in Hainan. SUSTAINABILITY 2022. [DOI: 10.3390/su14127415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural characteristics of the rhizosphere soil’s microbial community is crucial to understanding the ecological function of mangroves. However, the mechanism influencing mangrove plants in soil microbial communities has yet to be determined. Here, the mangrove ecosystem of Xinying Mangrove National Wetland Park in Hainan Province was taken as the research object. The microbial communities, external regulatory factors, and the relationship between communities were analyzed using 16S rRNA high-throughput sequencing in the rhizosphere and non-rhizosphere sediments of mangrove forests under different spatiotemporal conditions. The results showed that there was no significant difference in the α-diversity of the bacterial community between the rhizosphere and non-rhizosphere sediments. However, β-diversity was significantly different. Redundancy analysis (RDA) showed that other environmental factors besides sulfide and Fe2+ affected the bacterial community structure in sediments. The co-occurrence pattern analysis of bacteria in the mangrove ecosystem indicates that the bacteria in rhizosphere sediments were more closely related than those in non-rhizosphere sediments. The results reveal significant differences between the rhizosphere and non-rhizosphere bacterial community diversity, structure, and their interaction in the mangrove ecosystem. Therefore, the ecological system of the mangrove wetland needs to be preserved and rehabilitated, which would have a tremendous impact on the sustainable development.
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27
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Vadillo Gonzalez S, Clark GF, Johnston EL, Turney CSM, Fogwill CJ, Steinberg PD, Marzinelli EM. Spatial variation in microbial communities associated with sea-ice algae in Commonwealth Bay, East Antarctica. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35416764 DOI: 10.1099/mic.0.001176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antarctic sea-ice forms a complex and dynamic system that drives many ecological processes in the Southern Ocean. Sea-ice microalgae and their associated microbial communities are understood to influence nutrient flow and allocation in marine polar environments. Sea-ice microalgae and their microbiota can have high seasonal and regional (>1000 km2) compositional and abundance variation, driven by factors modulating their growth, symbiotic interactions and function. In contrast, our knowledge of small-scale variation in these communities is limited. Understanding variation across multiple scales and its potential drivers is critical for informing on how multiple stressors impact sea-ice communities and the functions they provide. Here, we characterized bacterial communities associated with sea-ice microalgae and the potential drivers that influence their variation across a range of spatial scales (metres to >10 kms) in a previously understudied area in Commonwealth Bay, East Antarctica where anomalous events have substantially and rapidly expanded local sea-ice coverage. We found a higher abundance and different composition of bacterial communities living in sea-ice microalgae closer to the shore compared to those further from the coast. Variation in community structure increased linearly with distance between samples. Ice thickness and depth to the seabed were found to be poor predictors of these communities. Further research on the small-scale environmental drivers influencing these communities is needed to fully understand how large-scale regional events can affect local function and ecosystem processes.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia.,Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW 2088, Australia
| | - Graeme F Clark
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2025, Australia
| | - Emma L Johnston
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2025, Australia
| | - Chris S M Turney
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2025, Australia.,University of Technology Sydney, 15 Broadway, Ultimo, NSW, 2007, Australia
| | - Christopher J Fogwill
- School of Geography, Geology and the Environment, Keele University, Keele ST5 5BG, UK.,School of Water, Energy and Environment, Building 52a, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Peter D Steinberg
- Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW 2088, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2025, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia.,Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW 2088, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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28
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Thomson T, Ellis JI, Fusi M, Prinz N, Bennett-Smith MF, Aylagas E, Carvalho S, Jones BH. The Right Place at the Right Time: Seasonal Variation of Bacterial Communities in Arid Avicennia marina Soils in the Red Sea Is Specific to Its Position in the Intertidal. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mangrove forests play an important role in facilitating biogeochemical pathways and cycling acting as blue carbon sinks. These services are primarily regulated by the activity of the soil microbiome. However, there is still limited research into spatial and temporal variation patterns of bacterial community assemblages in mangrove soils. This study investigated important ecological scales of microprocesses that govern microbial communities in an arid mangrove ecosystem. Shifts in microbial community composition were influenced by fluctuations in environmental factors within the mangrove forests of the Red Sea influenced by seasonal changes in sea level. Notably, in summer microbial communities in shrub sites differed significantly from the fringe and the winter samples, with lower alpha diversity yet a higher dominance of specialized species capable of surviving in extreme conditions. The onset of dispersal limitation and heterogenous selection and the reduction of drift are likely the main forces shaping community assemblages. Specifically, in summer lower mean tidal levels eliminate tidal inundation creating a harsh high salinity and high temperature environment with no tidal connection thereby influencing the onset of dispersal limitation. An increased understanding of the spatial and temporal variation of bacterial communities is critical when assessing delivery of ecosystem services and their role in soil biogeochemical processes.
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29
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Wood G, Steinberg PD, Campbell AH, Vergés A, Coleman MA, Marzinelli EM. Host genetics, phenotype and geography structure the microbiome of a foundational seaweed. Mol Ecol 2022; 31:2189-2206. [PMID: 35104026 PMCID: PMC9540321 DOI: 10.1111/mec.16378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2022] [Indexed: 12/01/2022]
Abstract
Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Peter D. Steinberg
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Alexandra H. Campbell
- USC Seaweed Research GroupUniversity of the Sunshine CoastSunshine CoastQueenslandAustralia
| | - Adriana Vergés
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- Department of Primary IndustriesNational Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
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30
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Thépot V, Slinger J, Rimmer MA, Paul NA, Campbell AH. Is the Intestinal Bacterial Community in the Australian Rabbitfish Siganus fuscescens Influenced by Seaweed Supplementation or Geography? Microorganisms 2022; 10:microorganisms10030497. [PMID: 35336073 PMCID: PMC8954549 DOI: 10.3390/microorganisms10030497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
We recently demonstrated that dietary supplementation with seaweed leads to dramatic improvements in immune responses in S. fuscescens, a candidate species for aquaculture development in Asia. Here, to assess whether the immunostimulatory effect was facilitated by changes to the gut microbiome, we investigated the effects of those same seaweed species and four commercial feed supplements currently used in aquaculture on the bacterial communities in the hindgut of the fish. Since we found no correlations between the relative abundance of any particular taxa and the fish enhanced innate immune responses, we hypothesised that S. fuscescens might have a core microbiome that is robust to dietary manipulation. Two recently published studies describing the bacteria within the hindgut of S. fuscescens provided an opportunity to test this hypothesis and to compare our samples to those from geographically distinct populations. We found that, although hindgut bacterial communities were clearly and significantly distinguishable between studies and populations, a substantial proportion (55 of 174 taxa) were consistently detected across all populations. Our data suggest that the importance of gut microbiota to animal health and the extent to which they can be influenced by dietary manipulations might be species-specific or related to an animals’ trophic level.
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Affiliation(s)
- Valentin Thépot
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
- Correspondence:
| | - Joel Slinger
- CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia;
- Institute of Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Michael A. Rimmer
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
| | - Nicholas A. Paul
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
| | - Alexandra H. Campbell
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia;
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31
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Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
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Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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32
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Jin J, Yamamoto R, Takeuchi T, Cui G, Miyauchi E, Hojo N, Ikuta K, Ohno H, Shiroguchi K. High-throughput identification and quantification of single bacterial cells in the microbiota. Nat Commun 2022; 13:863. [PMID: 35194029 PMCID: PMC8863893 DOI: 10.1038/s41467-022-28426-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota works as a community that consists of many individual organisms, i.e., cells. To fully understand the function of bacterial microbiota, individual cells must be identified; however, it is difficult with current techniques. Here, we develop a method, Barcoding Bacteria for Identification and Quantification (BarBIQ), which classifies single bacterial cells into taxa–named herein cell-based operational taxonomy units (cOTUs)–based on cellularly barcoded 16S rRNA sequences with single-base accuracy, and quantifies the cell number for each cOTU in the microbiota in a high-throughput manner. We apply BarBIQ to murine cecal microbiotas and quantify in total 3.4 × 105 bacterial cells containing 810 cOTUs. Interestingly, we find location-dependent global differences in the cecal microbiota depending on the dietary vitamin A deficiency, and more differentially abundant cOTUs at the proximal location than the distal location. Importantly, these location differences are not clearly shown by conventional 16S rRNA gene-amplicon sequencing methods, which quantify the 16S rRNA genes, not the cells. Thus, BarBIQ enables microbiota characterization with the identification and quantification of individual constituent bacteria, which is a cornerstone for microbiota studies. Here, Jin et al., develop a method called Barcoding Bacteria for Identification and Quantification (BarBIQ), which allows to both characterize the global microbiome and to identify and quantify single-cell bacterial members in a high-throughput manner.
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Affiliation(s)
- Jianshi Jin
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Reiko Yamamoto
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Tadashi Takeuchi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Guangwei Cui
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Eiji Miyauchi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Nozomi Hojo
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, 3-2-1, Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Katsuyuki Shiroguchi
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan.
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33
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Quek ZBR, Zahn G, Lee NLY, Ooi JLS, Lee JN, Huang D, Wainwright BJ. Biogeographic structure of fungal communities in seagrass Halophilia ovalis across the Malay Peninsula. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:871-877. [PMID: 34438473 DOI: 10.1111/1758-2229.13003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Distributed across both the tropical Atlantic and Pacific oceans, the seagrass Halophilia ovalis stabilizes coastal sediment, thereby preventing shoreline erosion and is also an important food source for megaherbivores such as dugongs. However, seagrass meadows globally are under severe duress due to both climate change and anthropogenic activities. We characterized the mycobiome of Halophilia ovalis at seven sites in the Malay Peninsula using ITS1 rDNA amplicon sequences and investigated differences in fungal community structure. We found that geographic location was a significant factor shaping fungal communities and that marine sediment harboured significantly higher diversity when compared to H. ovalis leaves, roots and rhizomes. Taken together, it is likely that locality rather than specific plant structure determines fungal community structure in H. ovalis. Because the plant mycobiome is known to exert a strong effect on plant health, to maximize the success of future seagrass transplantation and restoration work we propose that these efforts consider the importance of seagrass mycobiomes at all stages.
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Affiliation(s)
- Z B Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore
- Yale-NUS College, National University of Singapore, Singapore
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, Orem, UT, USA
| | - Nicole Li Ying Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jillian Lean Sim Ooi
- Department of Geography, Faculty of Arts and Social Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore
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34
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Whittle A, Barnett RL, Charman DJ, Gallego-Sala AV. Low-salinity transitions drive abrupt microbial response to sea-level change. Ecol Lett 2021; 25:17-25. [PMID: 34708510 DOI: 10.1111/ele.13893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022]
Abstract
The salinisation of many coastal ecosystems is underway and is expected to continue into the future because of sea-level rise and storm intensification brought about by the changing climate. However, the response of soil microbes to increasing salinity conditions within coastal environments is poorly understood, despite their importance for nutrient cascading, carbon sequestration and wider ecosystem functioning. Here, we demonstrate deterioration in the productivity of a top-tier microbial group (testate amoebae) with increasing coastal salinity, which we show to be consistent across phylogenetic groups, salinity gradients, environment types and latitude. Our results show that microbial changes occur in the very early stages of marine inundation, presaging more radical changes in soil and ecosystem function and providing an early warning of coastal salinisation that could be used to improve coastal planning and adaptation.
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Affiliation(s)
- Alex Whittle
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.,British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Robert L Barnett
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.,Département de biologie, chimie et géographie et Centre d'études nordiques, Université du Québec à Rimouski, Rimouski, Canada
| | - Dan J Charman
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Angela V Gallego-Sala
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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35
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De Santana CO, Spealman P, Melo V, Gresham D, de Jesus T, Oliveira E, Chinalia FA. Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary. PeerJ 2021; 9:e12229. [PMID: 34631324 PMCID: PMC8465992 DOI: 10.7717/peerj.12229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022] Open
Abstract
Mangroves are tropical ecosystems with strategic importance for climate change mitigation on local and global scales. They are also under considerable threat due to fragmentation degradation and urbanization. However, a complete understanding of how anthropogenic actions can affect microbial biodiversity and functional adaptations is still lacking. In this study, we carried out 16S rRNA gene sequencing analysis using sediment samples from two distinct mangrove areas located within the Serinhaém Estuary, Brazil. The first sampling area was located around the urban area of Ituberá, impacted by domestic sewage and urban runoff, while the second was an environmentally conserved site. Our results show significant changes in the structure of the communities between impacted and conserved sites. Biodiversity, along with functional potentials for the cycling of carbon, nitrogen, phosphorus and sulfur, were significantly increased in the urban area. We found that the environmental factors of organic matter, temperature and copper were significantly correlated with the observed shifts in the communities. Contributions of specific taxa to the functional potentials were negatively correlated with biodiversity, such that fewer numbers of taxa in the conserved area contributed to the majority of the metabolic potential. The results suggest that the contamination by urban runoff may have generated a different environment that led to the extinction of some taxa observed at the conserved site. In their place we found that the impacted site is enriched in prokaryotic families that are known human and animal pathogens, a clear negative effect of the urbanization process.
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Affiliation(s)
| | - Pieter Spealman
- Department of Biology, New York University, New York City, NY, United States of America
| | - Vania Melo
- Department of Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - David Gresham
- Department of Biology, New York University, New York City, NY, United States of America
| | - Taise de Jesus
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Eddy Oliveira
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
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36
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Duplouy A, Dotson BR, Nishiguchi MK, Cárdenas CA. Editorial: Symbiosis in a Changing Environment. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.731892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Salonen IS, Chronopoulou PM, Nomaki H, Langlet D, Tsuchiya M, Koho KA. 16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera. Front Microbiol 2021; 12:694406. [PMID: 34385987 PMCID: PMC8353385 DOI: 10.3389/fmicb.2021.694406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.
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Affiliation(s)
- Iines S Salonen
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland.,SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Dewi Langlet
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, Université de Lille - CNRS, Université du Littoral Côte d'Opale, Station Marine de Wimereux, Lille, France.,Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC), Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Karoliina A Koho
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland
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38
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Gadoin E, Durand L, Guillou A, Crochemore S, Bouvier T, d’Orbcastel ER, Dagorn L, Auguet JC, Adingra A, Desnues C, Bettarel Y. Does the Composition of the Gut Bacteriome Change during the Growth of Tuna? Microorganisms 2021; 9:1157. [PMID: 34072252 PMCID: PMC8229391 DOI: 10.3390/microorganisms9061157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, a growing number of studies sought to examine the composition and the determinants of the gut microflora in marine animals, including fish. For tropical tuna, which are among the most consumed fish worldwide, there is scarce information on their enteric bacterial communities and how they evolve during fish growth. In this study, we used metabarcoding of the 16S rDNA gene to (1) describe the diversity and composition of the gut bacteriome in the three most fished tuna species (skipjack, yellowfin and bigeye), and (2) to examine its intra-specific variability from juveniles to larger adults. Although there was a remarkable convergence of taxonomic richness and bacterial composition between yellowfin and bigeyes tuna, the gut bacteriome of skipjack tuna was distinct from the other two species. Throughout fish growth, the enteric bacteriome of yellowfin and bigeyes also showed significant modifications, while that of skipjack tuna remained relatively homogeneous. Finally, our results suggest that the gut bacteriome of marine fish may not always be subject to structural modifications during their growth, especially in species that maintain a steady feeding behavior during their lifetime.
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Affiliation(s)
- Elsa Gadoin
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Lucile Durand
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Aurélie Guillou
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Sandrine Crochemore
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Thierry Bouvier
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Emmanuelle Roque d’Orbcastel
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Laurent Dagorn
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | - Jean-Christophe Auguet
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
| | | | | | - Yvan Bettarel
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (E.G.); (L.D.); (A.G.); (S.C.); (T.B.); (E.R.d.); (L.D.); (J.-C.A.)
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39
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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40
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Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages. Microorganisms 2021; 9:microorganisms9020455. [PMID: 33671759 PMCID: PMC7927081 DOI: 10.3390/microorganisms9020455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.
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The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator. WATER 2021. [DOI: 10.3390/w13040406] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.
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Neu AT, Hughes IV, Allen EE, Roy K. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol 2021; 30:1237-1250. [PMID: 33432685 DOI: 10.1111/mec.15796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, is lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments: a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D.gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than ninefold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D.gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ian V Hughes
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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Morphological complexity affects the diversity of marine microbiomes. ISME JOURNAL 2020; 15:1372-1386. [PMID: 33349654 DOI: 10.1038/s41396-020-00856-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Large eukaryotes support diverse communities of microbes on their surface-epibiota-that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity-host evolutionary history and ecology, environmental conditions and stochasticity-do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.
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Garcias-Bonet N, Eguíluz VM, Díaz-Rúa R, Duarte CM. Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environ Microbiol 2020; 23:2021-2034. [PMID: 33225561 DOI: 10.1111/1462-2920.15334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, E-07122, Spain
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. mSystems 2020; 5:5/5/e00658-20. [PMID: 33082281 PMCID: PMC7577295 DOI: 10.1128/msystems.00658-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.
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Lee NLY, Huang D, Quek ZBR, Lee JN, Wainwright BJ. Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula. IMA Fungus 2020; 11:17. [PMID: 32974121 PMCID: PMC7493156 DOI: 10.1186/s43008-020-00042-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.
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Affiliation(s)
- Nicole Li Ying Lee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore.,Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227 Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia
| | - Benjamin J Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527 Singapore
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Proffitt C, Bidkhori G, Moyes D, Shoaie S. Disease, Drugs and Dysbiosis: Understanding Microbial Signatures in Metabolic Disease and Medical Interventions. Microorganisms 2020; 8:microorganisms8091381. [PMID: 32916966 PMCID: PMC7565856 DOI: 10.3390/microorganisms8091381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of the potential role for the gut microbiota in health and disease, many studies have gone on to report its impact in various pathologies. These studies have fuelled interest in the microbiome as a potential new target for treating disease Here, we reviewed the key metabolic diseases, obesity, type 2 diabetes and atherosclerosis and the role of the microbiome in their pathogenesis. In particular, we will discuss disease associated microbial dysbiosis; the shift in the microbiome caused by medical interventions and the altered metabolite levels between diseases and interventions. The microbial dysbiosis seen was compared between diseases including Crohn’s disease and ulcerative colitis, non-alcoholic fatty liver disease, liver cirrhosis and neurodegenerative diseases, Alzheimer’s and Parkinson’s. This review highlights the commonalities and differences in dysbiosis of the gut between diseases, along with metabolite levels in metabolic disease vs. the levels reported after an intervention. We identify the need for further analysis using systems biology approaches and discuss the potential need for treatments to consider their impact on the microbiome.
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Affiliation(s)
- Ceri Proffitt
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (G.B.); (D.M.)
- Correspondence: (C.P.); (S.S.)
| | - Gholamreza Bidkhori
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (G.B.); (D.M.)
| | - David Moyes
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (G.B.); (D.M.)
| | - Saeed Shoaie
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (G.B.); (D.M.)
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, 114 17 Stockholm, Sweden
- Correspondence: (C.P.); (S.S.)
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Coral Disease Causes, Consequences, and Risk within Coral Restoration. Trends Microbiol 2020; 28:793-807. [PMID: 32739101 DOI: 10.1016/j.tim.2020.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022]
Abstract
As a result of increased reef degradation, restoration efforts are now being widely applied on coral reefs. However, outplanted coral survival in restoration zones varies substantially, and coral mortality can be a significant limitation to the success of restoration efforts. With reef restoration now occurring within, and adjacent to, nationally preserved and managed marine parks, the potential risks of mortality events and disease spread to adjacent marine populations need to be considered, particularly as these ecosystems continue to decline. We review the causes and consequences of coral mortality and disease outbreaks within the context of coral restoration, highlighting knowledge gaps in our understanding of the restored coral microbiome and discussing management practices for assessing coral disease. We identify the need for research efforts into monitoring and diagnostics of disease within coral restoration, as well as practices to mitigate and manage coral disease risks in restoration.
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Cacabelos E, Ramalhosa P, Canning-Clode J, Troncoso JS, Olabarria C, Delgado C, Dobretsov S, Gestoso I. The Role of Biofilms Developed under Different Anthropogenic Pressure on Recruitment of Macro-Invertebrates. Int J Mol Sci 2020; 21:ijms21062030. [PMID: 32188145 PMCID: PMC7139543 DOI: 10.3390/ijms21062030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/29/2022] Open
Abstract
Microbial biofilms can be key mediators for settlement of macrofoulers. The present study examines the coupled effects of microbial biofilms and local environmental conditions on the composition, structure and functioning of macrofouling assemblages. Settlement of invertebrates over a gradient of human-impacted sites was investigated on local biofilms and on biofilms developed in marine protected areas (MPAs). Special attention was given to the presence of non-indigenous species (NIS), a global problem that can cause important impacts on local assemblages. In general, the formation of macrofouling assemblages was influenced by the identity of the biofilm. However, these relationships varied across levels of anthropogenic pressure, possibly influenced by environmental conditions and the propagule pressure locally available. While the NIS Watersipora subatra seemed to be inhibited by the biofilm developed in the MPA, Diplosoma cf. listerianum seemed to be attracted by biofilm developed in the MPA only under mid anthropogenic pressure. The obtained information is critical for marine environmental management, urgently needed for the establishment of prevention and control mechanisms to minimize the settlement of NIS and mitigate their threats.
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Affiliation(s)
- Eva Cacabelos
- MARE—Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo, Piso 0, Caminho da Penteada, 9020-105 Funchal, Madeira, Portugal
- Correspondence:
| | - Patrício Ramalhosa
- MARE—Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo, Piso 0, Caminho da Penteada, 9020-105 Funchal, Madeira, Portugal
- OMM—Oceanic Observatory of Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Edifício Madeira Tecnopolo, Piso 0, Caminho da Penteada, 9020-105 Funchal, Madeira, Portugal
| | - João Canning-Clode
- MARE—Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo, Piso 0, Caminho da Penteada, 9020-105 Funchal, Madeira, Portugal
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA
| | - Jesús S. Troncoso
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus As Lagoas-Marcosende, E-36310 Vigo, Galicia, Spain
- Centro de Investigación Marina, CIM Universidade de Vigo, Illa de Toralla, E-36331 Vigo, Galicia, Spain
| | - Celia Olabarria
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus As Lagoas-Marcosende, E-36310 Vigo, Galicia, Spain
- Centro de Investigación Marina, CIM Universidade de Vigo, Illa de Toralla, E-36331 Vigo, Galicia, Spain
| | - Cristina Delgado
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus As Lagoas-Marcosende, E-36310 Vigo, Galicia, Spain
| | - Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat 123, Oman
- Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Muscat 123, Oman
| | - Ignacio Gestoso
- MARE—Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo, Piso 0, Caminho da Penteada, 9020-105 Funchal, Madeira, Portugal
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA
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Vanwonterghem I, Webster NS. Coral Reef Microorganisms in a Changing Climate. iScience 2020; 23:100972. [PMID: 32208346 PMCID: PMC7096749 DOI: 10.1016/j.isci.2020.100972] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 01/09/2023] Open
Abstract
Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.
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Affiliation(s)
- Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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